One of our SharePoint servers at work was updated with the most recent round of security patches the other day. Unfortunately, the result of this update was the inability to login to the SharePoint Portal from the server, and the search crawler not being able to access the site.
After some significant research on the matter I came across http://support.microsoft.com/kb/896861 which indicates that an IIS website that is using Integrated Windows Authentication and the URL is different from the computer name, will result in a 401.1 error. The fix is to add the other names of the computer into a registry key and restart IIS. After following the instructions in the knowledge base article I was able to login to the site from the server, and the search crawler was once again able to crawl the content.